Cocoa (Theobroma cacao L.) pod husks are a secondary product of cocoa processing, thus presenting challenges regarding discarding and waste management. Proper waste management and efficient extraction methods for pectin from such agricultural waste are essential for promoting the principles of circular economy, which can offer several benefits. Thus, this study aimed to optimize pectin yield isolated from cocoa pod husks (CPH) under different conditions via the microwave-assisted extraction (MAE) method. Design Expert 11 was utilized to assess the impact of the response variables, namely microwave power (A), pH (B), and time (C) on the extraction yield. The study found that the pH and extraction time significantly affected the pectin yield (p < 0.05), whereas microwave power remained insignificant (p > 0.05). The yield ranged from 3.30 to 14.97% at the specified parameters and levels where the optimum result (14.92%) was achieved at pH, extraction time, and power levels of 1.0, 9 min, and 500 watts, respectively. The reduced model for pectin extraction was expressed in a coded equation, demonstrating the connections between pectin yield and the independent variables. The model demonstrated significance with a p-value of 0.0007. Under the optimized conditions, the physicochemical properties of the MAE pectin, namely ash content, moisture, equivalent weight, methoxyl content, anhydrouronic acid, and degree of esterification, were calculated at 5.72 ± 0.54%, 8.33 ± 0.42, 1044.66 ± 25.63, 5.02 ± 0.15, 75.62 ± 1.22, and 45.10 ± 1.60, respectively. Utilizing cocoa waste for pectin production promotes sustainable practices within the cocoa industry. It encourages stakeholders to adopt waste reduction strategies and invest in technologies for waste valorization, contributing to long-term environmental stewardship.